Files in rmflight/categoryCompare2
Meta-Analysis of High-Throughput Experiments Using Feature Annotations
.Rbuildignore
.Rinstignore
.github/workflows/r.yml
.gitignore
BUGS
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/all_classes.R
R/all_generics.R
R/annotations.R
R/binomial_enrichment.R
R/categoryCompare2.R
R/combine_enrichments.R
R/gocats.R
R/graph_table_annotation.R
R/graph_visualization.R
R/hypergeometric_enrichment.R
R/managing_annotations.R
R/significant_results.R
R/significant_results_calls.R
R/utils.R
README.md
exec/categoryCompare2.R
exec/create_annotations.R
exec/feature_files_2_json.R
exec/filter_and_group.R
exec/run_enrichment.R
executable_related/cc2_config.yml
executable_related/gene_files_2_json.R
executable_related/generate_test_data.R
executable_tests/executable_scripts.Rmd
executable_tests/test_executables.Rmd
inst/CITATION
inst/extdata/cc2_config.yml
inst/extdata/generate_test_data.R
inst/extdata/test_data/10_entrez.txt
inst/extdata/test_data/10_symbol.txt
inst/extdata/test_data/48_entrez.txt
inst/extdata/test_data/48_symbol.txt
inst/extdata/test_data/ancestors.json.gz
inst/extdata/test_data/create_annotations_example_input.json
inst/extdata/test_data/entrez.json
inst/extdata/test_data/namespace.json.gz
inst/extdata/test_data/universe_entrez.txt
inst/extdata/test_data/universe_symbol.txt
man/add_data_to_graph.Rd
man/add_tooltip.Rd
man/annotation.Rd
man/annotation_2_json.Rd
man/annotation_combinations.Rd
man/annotation_gene_table.Rd
man/assign_colors.Rd
man/assign_communities.Rd
man/binomial_basic.Rd
man/binomial_feature_enrichment.Rd
man/binomial_features-class.Rd
man/binomial_result-class.Rd
man/categoryCompare2.Rd
man/cc_graph.Rd
man/combine_annotation_features.Rd
man/combine_annotations.Rd
man/combine_enrichments.Rd
man/combine_text.Rd
man/combined_coefficient.Rd
man/combined_enrichment.Rd
man/combined_significant_calls.Rd
man/combined_statistics.Rd
man/csv_annotation_table.Rd
man/enriched_result.Rd
man/executable_path.Rd
man/extract_enrich_stats.Rd
man/extract_statistics-combined_enrichment-method.Rd
man/extract_statistics.Rd
man/filter_annotation_graph.Rd
man/generate_annotation_graph.Rd
man/generate_annotation_similarity_graph.Rd
man/generate_colors.Rd
man/generate_legend.Rd
man/generate_link.Rd
man/generate_piecharts.Rd
man/generate_table.Rd
man/get_db_annotation.Rd
man/get_significant_annotations.Rd
man/get_significant_annotations_calls.Rd
man/gocats_to_annotation.Rd
man/graph_to_visnetwork.Rd
man/hypergeom_features-class.Rd
man/hypergeometric_basic.Rd
man/hypergeometric_feature_enrichment.Rd
man/install_executables.Rd
man/jaccard_coefficient.Rd
man/json_2_annotation.Rd
man/json_annotation_reversal.Rd
man/kable_annotation_table.Rd
man/label_communities.Rd
man/multi_query_list.Rd
man/node_assign-class.Rd
man/overlap_coefficient.Rd
man/remove_edges.Rd
man/show-binomial_result-method.Rd
man/show-combined_statistics-method.Rd
man/show-enriched_result-method.Rd
man/show-node_assign-method.Rd
man/show-significant_annotations-method.Rd
man/significant_annotations.Rd
man/statistical_results-class.Rd
man/table_from_graph.Rd
man/vis_in_cytoscape.Rd
man/vis_visnetwork.Rd
project.Rproj
test_data_gen.R
test_data_gen2.R
tests.R
tests/testthat.R
tests/testthat/_snaps/binomial_enrichment.md
tests/testthat/_snaps/graph_creation.md
tests/testthat/_snaps/hypergeometric_enrichment.md
tests/testthat/combined_graph.rds
tests/testthat/enrichment_data.rds
tests/testthat/jaccard_graph.rds
tests/testthat/overlap_graph.rds
tests/testthat/test-binomial_enrichment.R
tests/testthat/test-combining_annotations.R
tests/testthat/test-getting_statistics.R
tests/testthat/test-gocats.R
tests/testthat/test-graph_creation.R
tests/testthat/test-hypergeometric_enrichment.R
tests/testthat/test-significant_results.R
vignettes/.gitignore
vignettes/BP2.png
vignettes/BP_8.png
vignettes/KEGG.png
vignettes/allEdges.png
vignettes/categoryCompare_vignette_v2.Rmd
vignettes/categoryCompare_vignette_v2_visnetwork.Rmd
vignettes/command_line_interface.Rmd
